Re: the safety of re-formatting with FAT32, Can I format SD to FAT32 from FAT16? discusses that a bit. I'm not sure that anyone can answer the "why" other than the manufacturer of the card (and, FWIW, the cards I've purchased have all been pre-formatted FAT32).
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eldarerathis♦May 20 '12 at 0:24

unless you have an sdcard that is 4gb or smaller, it is not formatted as FAT16. That is the max size for a fat16 volume.
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Ryan ConradMay 20 '12 at 1:05

The reason could have been that Android doesn't support FAT32, for example.
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ErikMay 20 '12 at 10:10

@SachinShekhar My android phone had this sd card FAT preformated. The actual filesize was around 500Mb and the size-on-disk because of the FAT was 1.3Gb. There should be a reason they ship a 2Gb formated that way. It takes space for no obvious reason.
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OdysMay 20 '12 at 10:16

2 Answers
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Generally FAT is used when possible simply because it's compatible with more (older) devices. While this is not much of an issue today, it probably continues out of (1) very slight market advantage and (2) the fact that factory machinery is set up that way and it would cost owners to change it.

In any event, Android can certainly read FAT32; if it couldn't nobody would be able to use SD cards larger than 2GB. There should be no problem with Android being able to read your card after a format.

I know it's an old question, but I just formatted a card (2GB) as FAT32. It was FAT(16) and at this size the total available space is reduced. Was 1.90GB, now 1.88GB. Now comes in the question of effeciency. Under FAT the files are in 32KB cluster. If you have text document, it is probably smaller than 32KB, but it will take up a full 32KB cluster. Under FAT32 the size should be around 4KB, that will be better for small files.